Collaborative Research: Unraveling Sulfur Networks in Methanogenic Archaea

合作研究：解开产甲烷古菌中的硫网络

• 批准号: 1632941
• 负责人: Yuchen Liu
• 金额: $ 25.74万
• 依托单位: Louisiana State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-01 至 2018-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1632941&HistoricalAwards=false
• 关键词: Collaborative; Research; Unraveling; Sulfur; Networks

Sulfur is an essential element for all known organisms and is present in amino acids, nucleotides and coenzymes. Because of its distinctive chemistry, it plays central roles in many essential biochemical pathways that likely evolved early in life's history, possibly around or before 3.5 Ga. At this time, the O2 concentrations were very low. Many sulfur-containing compounds in cells react with O2, and aerobic organisms possess highly conserved pathways for their biosynthesis that are compatible with an aerobic environment. The methanogenic archaea are an ancient lineage of strict anaerobes that never developed the ability to grow in the presence of O2. Their sulfur metabolism is also very distinctive, suggesting that they may possess pathways common before O2 became abundant in the biosphere. Unlike aerobes, most methanogenic archaea only use sulfide and elemental sulfur as the sulfur sources, and sulfate and other oxidized sulfur compounds are seldom utilized. Recent biochemical and genomics studies have revealed unusual features of their sulfur assimilation, including a unique tRNA-dependent cysteine biosynthesis pathway and the absence of canonical enzymes for Fe-S cluster and methionine biosynthesis. Thus, how sulfur is incorporated in methanogens remains unknown. Understanding the sulfur networks in methanogens will (i) advance our knowledge of the physiology of methanogens and how they are adapted to their unique ecological niche; (ii) discover novel enzymes and pathways of sulfur metabolism that may be common in other anaerobes; (iii) provide a more complete picture of sulfur chemistry in life and the evolution of the sulfur cycle on the early, anaerobic Earth; and (iv) guide engineering of methanogens for production of methane, a carbon neutral biofuel. Integrated into these scientific goals will be interdisciplinary training of the next generation of scientists, including high school, undergraduate and graduate students, and a young investigator.Technical description: Sulfur is essential for the growth of all known organisms and is present in a wide variety of molecules with different physiological functions. Consistent with their strictly anaerobic lifestyle, most methanogenic archaea only use sulfide and elemental sulfur as sulfur sources, and sulfate and other oxidized sulfur compounds are seldom utilized. Recent studies have revealed novel features of sulfur assimilation in the methanogenic archaeon Methanococcus maripaludis. These include: homologs of many sulfur metabolic genes common in bacteria and eukaryotes are absent; cysteine is biosynthesized by a novel tRNA-dependent pathway; cysteine is not an intermediate for Fe-S cluster, methionine and 4-thiouridine biosynthesis; and the sulfur transfer motif of the 4-thiouridine synthetase is distinct from that found in bacteria. These discoveries greatly broadened our view of physiological sulfur chemistry. However, many aspects of the sulfur transfer processes in methanococci remain to be elucidated. An important question is whether sulfide is directly used as the sulfur donor in various pathways or unique sulfur carrier proteins are involved in sulfur relay. This research specifically seeks to understand (i) the physiological sulfur transfer mechanism of tRNA-dependent cysteine biosynthesis; (ii) the sulfur relay system of the archaeal ubiquitin-like pathway for tRNA 2-thiouridine biosynthesis; (iii) the enzymes and carriers in a global sulfur metabolic network; and (iv) the intracellular levels of sulfide available for these biochemical systems. Research on sulfur networks will advance our knowledge of the physiology of methanogens and how they are adapted to their unique ecological niche. Since sulfate was limited on the early, anoxic Earth while sulfide and elemental sulfur were presumably abundant, methanogens that assimilate sulfide and elemental sulfur as sole sulfur sources provide a living window into the primitive sulfur metabolism and shed light on the evolutionary processes of early Earth. Furthermore, most of our knowledge on sulfur assimilation is based upon aerobes and facultative anaerobes. As many of the known sulfur transfer enzymes from bacteria and eukaryotes are missing in methanogens, the elucidation of sulfur relay in methanogens may guide discovery of novel sulfur metabolic pathways that may be common in other anaerobes; this will contribute to a more complete understanding of sulfur chemistry in life. The broader impacts of this work include the following. (i) Unraveling S metabolism in methanogens will assist modeling of their metabolism and bioengineering the production of methane, a carbon neutral biofuel. (ii) It will provide new insights into mechanisms to control emissions of methane, a potent greenhouse gas that contributes to global warming. (iii) This study will develop a new genome-wide screening method, which will be of great value for systematic discoveries of novel pathways in an archaeal model organism. (iv) This project will provide interdisciplinary training to the next generation of scientists, including high school, undergraduate and graduate students, in microbial physiology, biochemistry and genetics. It will encourage students to view the entirety of the organism as it exists within a specific ecological context. (v) It will establish a path to independence for the CoPI Dr. Liu, a young investigator.

硫是所有已知生物的重要元素，并且存在于氨基酸，核苷酸和辅酶中。 由于其独特的化学反应，它在许多基本生物化学途径中起着核心作用，这些途径可能在生命的历史早期，可能在3.5 GA之前或之前在3.5 GA之前发展起来，此时，O2浓度非常低。 细胞中的许多含硫化合物与O2反应，有氧生物具有高度保守的生物合成途径，它们与有氧环境兼容。 甲烷古细菌是严格的厌氧菌的古老谱系，在O2存在下从未发展出生长的能力。 它们的硫代谢也非常独特，这表明它们在O2在生物圈中变得丰富之前可能具有常见的途径。 与健全不同，大多数甲烷古细菌仅将硫化物和元素硫作为硫来源，而硫酸盐和其他氧化的硫化合物很少被使用。 最近的生化和基因组学研究揭示了其硫同化的异常特征，包括独特的tRNA依赖性半胱氨酸生物合成途径，以及缺乏用于Fe-S簇和甲硫氨酸生物合成的规范酶。 因此，如何将硫掺入甲烷剂中仍然未知。 了解甲烷剂中的硫网络将（i）提高我们对甲烷剂生理学的了解，以及如何适应其独特的生态位； （ii）发现新的酶和硫代谢的途径，这些酶在其他厌氧菌中可能很常见； （iii）在生命中提供了更完整的硫化学和早期硫循环演化的图像； （iv）指导甲烷生产甲烷的工程，甲烷，一种中性生物燃料。 融入这些科学目标的是对下一代科学家的跨学科培训，包括高中，本科生和研究生，以及年轻的研究者。技术描述：硫对于所有已知生物的生长至关重要，并且具有不同生理功能的各种分子。 与严格的厌氧生活方式一致，大多数甲烷古细菌仅将硫化物和元素硫作为硫来源，而硫酸盐和其他氧化硫化合物很少被使用。 最近的研究揭示了甲烷源性甲烷甲球菌中硫同化的新特征。 其中包括：在细菌和真核生物中常见的许多硫代谢基因的同源物；半胱氨酸是通过一种新型的tRNA依赖性途径生物合成的。半胱氨酸不是Fe-S簇，蛋氨酸和4-硫脲生物合成的中间体。 4-硫脲合成酶的硫转移基序与细菌中的硫转移基序不同。 这些发现极大地扩大了我们对生理硫化学的看法。 然而，甲氧球菌中硫转移过程的许多方面仍有待阐明。 一个重要的问题是，硫化物是否直接用作各种途径中的硫供体，还是独特的硫载体蛋白参与硫继电器。 这项研究专门旨在理解（i）依赖于tRNA的半胱氨酸生物合成的生理硫转移机制； （ii）用于tRNA 2-硫脲生物合成的古细胞泛素样途径的硫磺继电系统； （iii）全球硫代谢网络中的酶和载体； （iv）可用于这些生化系统的细胞内硫化物水平。对硫网络的研究将提高我们对甲烷剂生理学的了解，以及它们如何适应其独特的生态位。 由于硫酸盐在早期受到限制，而硫化物和元素硫的含量大概是丰富的，因此甲烷元素吸收了硫化物和元素硫，因为唯一的硫来源为原始的硫代谢提供了一个活的窗口，并阐明了地球早期进化过程。 此外，我们关于硫同化的大多数知识都是基于健美动物和兼性厌氧菌。 由于来自细菌和真核生物中的许多已知的硫转移酶在甲烷剂中缺少，因此甲基元素中硫磺继电器的阐明可以指导发现在其他厌氧菌中可能常见的新型硫代谢途径的发现。这将有助于对生活中的硫化学有更全面的了解。 这项工作的更广泛影响包括以下内容。 （i）甲烷剂中的S新陈代谢将有助于建模其代谢和生物工程甲烷的生产，甲烷（一种碳中性生物燃料）。 （ii）它将为控制甲烷排放的机制提供新的见解，甲烷的排放是一种有效的温室气体，有助于全球变暖。 （iii）这项研究将开发一种新的全基因组筛查方法，这对于在古细菌模型生物中的新途径的系统发现具有巨大价值。 （iv）该项目将向下一代科学家（包括高中，本科生和研究生，微生物生理学，生物化学和遗传学）提供跨学科的培训。 它将鼓励学生在特定的生态环境中查看其整个生物体。 （v）它将为年轻的调查员刘·刘博士建立独立的途径。

项目成果

A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes

• DOI: 10.1073/pnas.1615732113
• 发表时间: 2016-11-08
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Liu, Yuchen;Vinyard, David J.;Soll, Dieter
• 通讯作者: Soll, Dieter